Personal genomics

From Asiangenome.org

Personal genomics is a branch of genomics where individual genomes are genotyped and analyzed using bioinformatics tools. It is also related to traditional population genetics. The genotyping stage can have many different experimental approaches including single nucleotide polymorphism (SNP) chips (typically 0.02% of the genome), or partial or full genome sequencing. Once the genotypes are known, there are many bioinformatics analysis tools that can compare individual genomes and find disease association of the genes and loci. The most important aspect of personal genomics is that it leads to the personal medicine where patients can take genotype specific drugs for medical treatments.

Personal genomics is not a single individual's vision or invention. Many researchers for decades anticipated this biological branch will eventually arrive with minimum cost of genotyping. Due to the advent of cheap and fast sequencers, full genome personal genomics is becoming a reality. However, there have been active early proponents of personal genomics projects such as George Church in Harvard Medical School.

Genomics used to mean academic research on consensus genomes which have been assembled from many different individuals of a particular species. The personal genomics changes this into customized bioinformatic discovery on individuals.

Use of personal genomics in personalized medicine

Personalized medicine is the use of the information produced by personal genomics techniques when deciding what medical treatments are appropriate for a particular individual.

An example of the use of personalized medicine is in selecting which drug to prescribe to a patient. The drug should be chosen to maximize the probability of obtaining the desired result in the patient and minimizing the probability that the patient will experience side effects.

The probabilities of obtaining the desired result and of experiencing side effects are both dependent on information that can be obtained by analysis of the patient’s genome.

Genomics is itself a rapidly developing field. As new techniques are developed in genomics it is likely that some of them will be applied in personal genomics and personalized medicine.

Cost of sequencing an individual’s genome

There is currently great interest in personal genomics. This is being fuelled by the rapid drop in the cost of sequencing a human genome. This drop in cost is due to the continual development of new, faster, cheaper DNA sequencing technologies such as "next generation DNA sequencing".

The National Human Genome Research Institute, part of the U.S. National Institute of Health has set a target to be able to sequence a human-sized genome for US$100,000 by 2009 and US$1,000 by 2014[1]. There is a widespread belief that within 10 years the cost of sequencing a human genome will fall to $1,000.

There are 6 billion base pairs in the diploid human genome. Statistical analysis reveals that a coverage of approximately ten times is required to get coverage of both alleles in 90% human genome from 25 base-pair reads with shotgun sequencing[2]. This means a total of 60 billion base pairs that must be sequenced. An ABI SOLiD, Illumina or Helicos[3] sequencing machine can sequence 2 to 10 billion base pairs in each $8,000 to $18,000 run. The purchase cost, personnel costs and data processing costs must also be taken into account. Sequencing a human genome therefore costs approximately $300,000 in 2008.

This cost is still too high for governments to introduce programs into health services to sequence the genomes of all individuals in a country. However, it may be viable when it falls below $1,000, and the cost of sequencing a human genome is dropping rapidly. For example, approximately 1 million babies are born in Canada each year. To sequence all of their genomes would cost approximately $1 billion per year, or just 1% of Canada’s total healthcare budget.

Comparative genomics

Comparative genomics analysis is concerned with characterising the differences and similarities between whole genomes. It may be applied to both genomes from individuals from different species or individuals from the same species, generally at lower cost than sequencing from scratch. In personal genomics and personalized medicine, we are concerned with comparing the genomes of different humans. It is likely that many of the techniques which are developed in comparative genomic analysis will be useful in personal genomics and personalized medicine. This includes rare and common Single nucleotide polymorphisms (consisting substituting one base pair by another, for example CATGCCGG to CATGACGG), as well as insertion or deletion of one or many base pairs.

Personalized medicine services already available

At least four companies which offer genome-wide personal genomics services already exist. They are likely to be the first of many.

23andMe sells mail order kits for SNP genotyping[4]. The $399 kit contains everything a patient needs to take their own saliva sample. The patient then mails the sample to 23andMe who carry out microarray analysis on it. This provides genotype information for about 600,000 SNPs. This information is used to estimate the genetic risk of the patient for over 80 diseases as well as ancestry analyses.

deCODEme.com[5] offers a similar service to 23andMe, charging $985 to carry out an analysis of approximately 1 million SNPs and estimate the risk of 29 diseases.

Navigenics[6], began offering SNP-based genomic risk assessments as of April 2008. Navigenics is medically focused and emphasizes a clinician's and genetic counselor's role in interpreting results. Currently over 20 disease are offered for $2500, with more in the works. [7]. Navigenics uses Affymetrix Genome-Wide Human SNP Array 6.0 , which tests some 900,000 SNPs. [8]

Promethease is a free program that uses all the information generated by companies like those mentioned above to prepare a personal report based on analyzing personal DNA data in light of all the information in SNPedia, the wiki of SNP data from scientific and medical articles

Ethical issues

While personalized medicine will certainly be a great asset to healthcare, it opens up several ethical issues which will need to be thought about carefully. No doubt there will be a huge amount of debate concerning the ethics of personalised medicine in the coming years.

Genetic discrimination is discriminating on the grounds of information obtained from an individual’s genome. Genetic non-discrimination laws have been enacted in most US states and, at the federal level, by the Genetic Information Nondiscrimination Act (GINA).

The likelihood of an individual developing breast cancer is affected by which alleles they have of particular genes. Screening can reveal breast cancer in the early stages, allowing it to be successfully treated. 50% of breast cancers occur in the 12% of the population who are at greatest risk. This poses a very difficult question for health services: Is it ethical to deny somebody free screening for a disease if they are genetically at low risk of developing that disease?

See also

Human genome map

Single nucleotide polymorphism

Population genomics

Bioinformatics

Genomics

Systems biology

Transcriptomics

Omics

References

^ Coming Soon: Your Personal DNA Map?

^ Table 4. Fractions of Heterozygotes as a function of Shotgun coverage(redundancy)